In this paper, a detailed study to probe the top quark Flavour-Changing Neutral Currents (FCNC) and at the future collider FCC-ee in three different center-of-mass energies of 240, 350 and 500 GeV is presented. A set of useful variables are proposed and used in a multivariate technique to separate signal $e^- e^+ \rightarrow Z/\gamma \rightarrow t \bar{q} ~ ( \bar{t} q )$ from standard model background processes. The study includes a fast detector simulation based on the {\sc delphes} package to consider the detector effects. The discovery regions and the upper limits on the FCNC branching ratios at 95% confidence level (CL) in terms of the integrated luminosity are presented. It is shown that with 300 fb of integrated luminosity of data, FCC-ee would be able to exclude the effective coupling strengths above which is corresponding to branching fraction of %. We show that moving to a high-luminosity regime leads to a significant improvement on the upper bounds on the top quark FCNC couplings to a photon or a boson.

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